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Table 3 Variants in risk-associated genes

From: A neurodegenerative disease landscape of rare mutations in Colombia due to founder effects

Gene Coding change dbSNP/ClinVar Classification ExAC 1000G CADD Local ancestry
ABCA7 c.2T>C rs1347920426 PTV (nonsense) . . 24.9 Native American
c.236A>C (p.Asn79Thr) rs377401443 SD 4.16E-05 . 24.5 African
c.1180_1190del (p.Leu396fs) rs567222111 PTV (frameshift) 0.0005 0.0022 . African
c.1531G>T (p.Glu511*) rs374932832 PTV (nonsense) 7.60E-05 . 39 African
c.1776G>T (p.Trp592Cys) SCV001751545 SD . . 26 African
c.2124_2130del (p.Glu709fs)+ rs547447016 PTV (frameshift) 0.0024 0.0006 . European
c.2194C>T (p.Gln732*) rs1030634619 PTV (nonsense) . . 36 European
c.2552+11_2552+58del rs1178315251 PTV (splice) . . . African
c.2611G>C (p.Asp871His) rs139251928 SD 0.0004 0.0014 24.8 African
c.3781delC (p.Pro1261fs) SCV001751546 PTV (frameshift)    . Native American
c.4208delT (p.Leu1403fs) rs538591288 PTV (frameshift) 0.0011 . . European
c.4465C>T (p.Arg1489*) rs753664323 PTV (nonsense) 6.66E-05 . 39 European
c.4886C>T (p.Ser1629Leu)+ rs184590335 SD 0.0012 0.0006 35 Native American
c.4895C>T (p.Pro1632Leu) rs143083561 SD 0.0002 0.0006 34 African
c.5302delC (p.Leu1768fs) rs1348650979 PTV (frameshift) . . . Native American
c.5463+2T>C rs374611445 PTV (splice) 2.81E-05 . 23.7 European
c.5794C>T (p.Arg1932C) rs114787084 SD 0.0002 0.0006 34 African
SORL1 c.994C>T (p.Arg332Trp) rs772110877 SD 5.77E-05 . 35 European
c.1432G>C (p.Ala478Pro) SCV001751547 SD . . 28.2 European
c.1496C>T (p.Ser499Leu) rs764032259 SD 8.24E-06 . 35 European
c.2200G>A (p.Asp734Asn) rs148430425 SD 0.0011 . 34 European
c.2230C>T (p.Arg744*) rs1050845490 PTV (nonsense) . . 39 European
c.2710C>T (p.Arg904Trp) rs148966249 SD 4.12E-05 2.00E-04 33 Native American
c.3679G>T (p.Gly1227Cys) rs1765488318 SD . . 34 European
c.4520C>T (p.Pro1507Leu) rs1308522330 SD . . 26.2 Undetermined
c.6550G>A (p.Ala2184Thr) rs369618646 SD 4.16E-05 . 34 African
TREM2 c.140G>A (p.Arg47His)+ rs75932628 SD 0.0021 0.002 33 European
c.469C>T (p.His157Tyr)+ rs2234255 SD 0.0036 0.0028 23.1 Native American
NM_001271821
c.287C>A (p.Thr96Lys)
c.572G>A(p.Trp191*)
c.632T>C (p.Leu211Pro)
rs2234253
rs2234258
rs2234256
PTV (nonsense)     African
c.594G>A (p.Trp198*) rs1765488318 PTV (nonsense) . . 39 Undetermined
ADAM10 c.510G>C (p.Gln170His)+ rs61751103 SD 0.0012 0.0012 19.17 European
  1. PTV protein truncating variant, SD strictly damaging, ExAC ExAC database minor allelic frequency. CADD corresponds to the Phred score. Variants denoted with a + were identified in homozygous states. GenBank transcripts for each gene can be found in Additional file 4: Table S3